Agents in Biology
191
12,000 iteration steps representing two hours of the stochastic equation model.
The other rates used in the model were as follows:
• SOURCE DECAY RATE 0.01 - The decay rate of the source.
• SOURCE TIME DECAY 8640 - The time step at which source will start
decaying represents 144 minutes of the stochastic simulation.
• SOURCE TIME PRODUCE 50 - The time after which the source will
start producing a protein.
• SOURCE PRODUCTION PROB 1.0 - The production probability of a
protein
• PROTEIN DECAY RATE 0.01 - The decay rate of the protein.
• COMPARTMENT DIMENSION X 5 - The dimension width of a compartment.
• COMPARTMENT DIMENSION Y 15 - The dimension height of a compartment.
• PROB RIGHT 0.5 - The probability of a protein to move right to the
compartment on the right.
• PROB LEFT 0.1 - The probability of a protein to move left to the
compartment of the left. The probability to move right was kept higher
as this would be more favourable.
• DIE 0.001 - Numerical value to denote when a life goes below this value,
kill the agent.
The values for probabilities of source production rates, protein decay rates,
right and left movement probability are conditions that will be changed which
each experimental run. Changing these conditions can allow results to be
mapped to the stochastic results, in order to find optimum rates which produce
the same results. The code for the agent functions is as follows:
/**** Compartment Agent Functions **********/
int Compartment_calculateproteins()
{
int protein_ct=0;
protein_location_message=get_first_protein_location_message();
while(protein_location_message)
{
if((protein_location_message->y>Y0)&&(protein_location_message->y {
protein_ct++;
}
if(protein_location_message->compartment==ID)
{
protein_ct++;